/*  sam_internal.h -- internal functions; not part of the public API.

    Copyright (C) 2019-2020, 2023-2024 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

DEALINGS IN THE SOFTWARE.  */

#ifndef HTSLIB_SAM_INTERNAL_H

#define HTSLIB_SAM_INTERNAL_H

#include <errno.h>

#include <stdint.h>

#include "htslib/sam.h"

#ifdef __cplusplus

extern "C" {

#endif

// Used internally in the SAM format multi-threading.

int sam_state_destroy(samFile *fp);

int sam_set_thread_pool(htsFile *fp, htsThreadPool *p);

int sam_set_threads(htsFile *fp, int nthreads);

// Fastq state

int fastq_state_set(samFile *fp, enum hts_fmt_option opt, ...);

void fastq_state_destroy(samFile *fp);

// bam1_t data (re)allocation

int sam_realloc_bam_data(bam1_t *b, size_t desired);

static inline int realloc_bam_data(bam1_t *b, size_t desired)

{

    if (desired <= b->m_data) return 0;

    return sam_realloc_bam_data(b, desired);

}

Unexecuted instantiation: hts.c:realloc_bam_data

sam.c:realloc_bam_data

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48

5.84M

{

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5.84M

    if (desired <= b->m_data) return 0;

50

635k

    return sam_realloc_bam_data(b, desired);

51

5.84M

}

Unexecuted instantiation: simd.c:realloc_bam_data

Unexecuted instantiation: cram_encode.c:realloc_bam_data

static inline int possibly_expand_bam_data(bam1_t *b, size_t bytes) {

    size_t new_len = (size_t) b->l_data + bytes;

    if (new_len > INT32_MAX || new_len < bytes) { // Too big or overflow

        errno = ENOMEM;

        return -1;

    }

    if (new_len <= b->m_data) return 0;

    return sam_realloc_bam_data(b, new_len);

}

Unexecuted instantiation: hts.c:possibly_expand_bam_data

sam.c:possibly_expand_bam_data

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53

6.51M

static inline int possibly_expand_bam_data(bam1_t *b, size_t bytes) {

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    size_t new_len = (size_t) b->l_data + bytes;

55

56

6.51M

    if (new_len > INT32_MAX || new_len < bytes) { // Too big or overflow

57

0

        errno = ENOMEM;

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0

        return -1;

59

0

    }

60

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    if (new_len <= b->m_data) return 0;

61

18.0k

    return sam_realloc_bam_data(b, new_len);

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6.51M

}

Unexecuted instantiation: simd.c:possibly_expand_bam_data

Unexecuted instantiation: cram_encode.c:possibly_expand_bam_data

/*

 * Convert a nibble encoded BAM sequence to a string of bases.

 *

 * We do this 2 bp at a time for speed. Equiv to:

 *

 * for (i = 0; i < len; i++)

 *    seq[i] = seq_nt16_str[bam_seqi(nib, i)];

 */

static inline void nibble2base_default(uint8_t *nib, char *seq, int len) {

    static const char code2base[512] =

        "===A=C=M=G=R=S=V=T=W=Y=H=K=D=B=N"

        "A=AAACAMAGARASAVATAWAYAHAKADABAN"

        "C=CACCCMCGCRCSCVCTCWCYCHCKCDCBCN"

        "M=MAMCMMMGMRMSMVMTMWMYMHMKMDMBMN"

        "G=GAGCGMGGGRGSGVGTGWGYGHGKGDGBGN"

        "R=RARCRMRGRRRSRVRTRWRYRHRKRDRBRN"

        "S=SASCSMSGSRSSSVSTSWSYSHSKSDSBSN"

        "V=VAVCVMVGVRVSVVVTVWVYVHVKVDVBVN"

        "T=TATCTMTGTRTSTVTTTWTYTHTKTDTBTN"

        "W=WAWCWMWGWRWSWVWTWWWYWHWKWDWBWN"

        "Y=YAYCYMYGYRYSYVYTYWYYYHYKYDYBYN"

        "H=HAHCHMHGHRHSHVHTHWHYHHHKHDHBHN"

        "K=KAKCKMKGKRKSKVKTKWKYKHKKKDKBKN"

        "D=DADCDMDGDRDSDVDTDWDYDHDKDDDBDN"

        "B=BABCBMBGBRBSBVBTBWBYBHBKBDBBBN"

        "N=NANCNMNGNRNSNVNTNWNYNHNKNDNBNN";

    int i, len2 = len/2;

    seq[0] = 0;

    for (i = 0; i < len2; i++)

        // Note size_t cast helps gcc optimiser.

        memcpy(&seq[i*2], &code2base[(size_t)nib[i]*2], 2);

    if ((i *= 2) < len)

        seq[i] = seq_nt16_str[bam_seqi(nib, i)];

}

Unexecuted instantiation: hts.c:nibble2base_default

Unexecuted instantiation: sam.c:nibble2base_default

simd.c:nibble2base_default

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72

1.70M

static inline void nibble2base_default(uint8_t *nib, char *seq, int len) {

73

1.70M

    static const char code2base[512] =

74

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        "===A=C=M=G=R=S=V=T=W=Y=H=K=D=B=N"

75

1.70M

        "A=AAACAMAGARASAVATAWAYAHAKADABAN"

76

1.70M

        "C=CACCCMCGCRCSCVCTCWCYCHCKCDCBCN"

77

1.70M

        "M=MAMCMMMGMRMSMVMTMWMYMHMKMDMBMN"

78

1.70M

        "G=GAGCGMGGGRGSGVGTGWGYGHGKGDGBGN"

79

1.70M

        "R=RARCRMRGRRRSRVRTRWRYRHRKRDRBRN"

80

1.70M

        "S=SASCSMSGSRSSSVSTSWSYSHSKSDSBSN"

81

1.70M

        "V=VAVCVMVGVRVSVVVTVWVYVHVKVDVBVN"

82

1.70M

        "T=TATCTMTGTRTSTVTTTWTYTHTKTDTBTN"

83

1.70M

        "W=WAWCWMWGWRWSWVWTWWWYWHWKWDWBWN"

84

1.70M

        "Y=YAYCYMYGYRYSYVYTYWYYYHYKYDYBYN"

85

1.70M

        "H=HAHCHMHGHRHSHVHTHWHYHHHKHDHBHN"

86

1.70M

        "K=KAKCKMKGKRKSKVKTKWKYKHKKKDKBKN"

87

1.70M

        "D=DADCDMDGDRDSDVDTDWDYDHDKDDDBDN"

88

1.70M

        "B=BABCBMBGBRBSBVBTBWBYBHBKBDBBBN"

89

1.70M

        "N=NANCNMNGNRNSNVNTNWNYNHNKNDNBNN";

90

91

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    int i, len2 = len/2;

92

1.70M

    seq[0] = 0;

93

94

3.37M

    for (i = 0; i < len2; i++)

95

        // Note size_t cast helps gcc optimiser.

96

1.66M

        memcpy(&seq[i*2], &code2base[(size_t)nib[i]*2], 2);

97

98

1.70M

    if ((i *= 2) < len)

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204k

        seq[i] = seq_nt16_str[bam_seqi(nib, i)];

100

1.70M

}

Unexecuted instantiation: cram_encode.c:nibble2base_default

#if defined HAVE_ATTRIBUTE_CONSTRUCTOR && \

    ((defined __x86_64__ && defined HAVE_ATTRIBUTE_TARGET_SSSE3 && defined HAVE_BUILTIN_CPU_SUPPORT_SSSE3) || \

     (defined __ARM_NEON))

#define BUILDING_SIMD_NIBBLE2BASE

#endif

static inline void nibble2base(uint8_t *nib, char *seq, int len) {

#ifdef BUILDING_SIMD_NIBBLE2BASE

    extern void (*htslib_nibble2base)(uint8_t *nib, char *seq, int len);

    htslib_nibble2base(nib, seq, len);

#else

    nibble2base_default(nib, seq, len);

#endif

}

Unexecuted instantiation: hts.c:nibble2base

sam.c:nibble2base

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108

185k

static inline void nibble2base(uint8_t *nib, char *seq, int len) {

109

185k

#ifdef BUILDING_SIMD_NIBBLE2BASE

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    extern void (*htslib_nibble2base)(uint8_t *nib, char *seq, int len);

111

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    htslib_nibble2base(nib, seq, len);

112

#else

113

    nibble2base_default(nib, seq, len);

114

#endif

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}

Unexecuted instantiation: simd.c:nibble2base

cram_encode.c:nibble2base

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108

1.51M

static inline void nibble2base(uint8_t *nib, char *seq, int len) {

109

1.51M

#ifdef BUILDING_SIMD_NIBBLE2BASE

110

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    extern void (*htslib_nibble2base)(uint8_t *nib, char *seq, int len);

111

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    htslib_nibble2base(nib, seq, len);

112

#else

113

    nibble2base_default(nib, seq, len);

114

#endif

115

1.51M

}

#ifdef __cplusplus

}

#endif

#endif